Paved with good intentions
by Pranksta
Summary: Pain comes, drenches him with the memory of grief, and he knows that time does not heal all wounds.
1. Chapter 1

Unnecessarily long A/N: I've been working on this since July and it's been driving me crazy, or crazier. I can't decide if it went the good or horrible way, so I'll leave it up to you. Please, comment freely, I would be very –very, very, very – interested in what you have to say, good or bad. Don't be afraid to say you disliked it; I would love to know why. 

**Genre: **Gen; drama, angst  
**Characters: **McKay – Sheppard friendship with a bit of Carson.  
**Word Count:** 14000 words  
**Rating:** High, for sensitive situation and cursing.  
**Warnings: DARK! Death of major character**.  
**Summary:** Pain comes, drenches him with the memory of grief, and he knows that time does not heal all wounds.  
**Beta: **The ever-so-wonderful Angela and Cheryl. Thank you so much for the hand-holding, the honest opinion and the time. I can't even begin to tell you how much I appreciate your help with this. You are truly great women, and I don't know what I did to deserve you two, but I sure hope I keep doing it!

**Chapter 1: A day in the life**

John Sheppard opens his eyes. He turns over slowly and blinks at the alarm clock. It blinks back: 7:59. A few seconds and the grating voice of the morning DJ will blast its way to his sleep-addled mind. It's warm under the sheet, so John allows himself the extra seconds. His head returns to the cushioning of goose down. Too fast, the click comes, and what reaches him is not the screams of over-caffeinated morning people, but a punch in the gut softened by a melody.

_Once there was a way, to get back homeward.  
Once there was a way, to get back home._

As Paul McCartney's voice flows over him, John pushes his head further into the pillow, brings the sheet over his head, and hopes this isn't happening.

Hopes this isn't the day, and though he knows he has to get up and face it, he cannot bring himself to leave the safety of his bed. He longs for the mindlessness of sleep.

It seems he is getting a two-for-one on this merry morning.

_Boy, you're gonna carry that weight, carry that weight a long time.  
Boy, you're gonna carry that weight, carry that weight a long time._

Pain comes, drenches him with the memory of grief and he knows that time does not heal all wounds. A shower, coffee and breakfast, however, might temporarily distract him.

**O-O-O-O-O**

"No! Don't touch that!" McKay slapped Sheppard's hand away.

"What! It's asking me to!"

"It's not asking you to do anything. You've just convinced yourself that Ancient technology talks to you because you think it's cool. It's not cool, the technology is not talking to you, Atlantis is not in love with you, or Carson – and I said don't touch that!"

"What!?"

"Don't touch anything! You're always telling me to be careful; I'm telling you to back the hell away."

"You're no fun." Sheppard grinned behind McKay's back, but catching Teyla's disapproving look somewhat lessened the glow of pleasure he got from annoying Rodney to an inch of his life. He shrugged and stepped away.

"I'm plenty of fun, thank you very much. I simply happen to enjoy being alive, and would like to keep it that way if you don't mind, so don't. Touch. Anything!"

Just a normal exploration day in Atlantis. Sheppard _knew _one should never think things like that, especially one who lived in the Pegasus galaxy and was rumoured to have a cursed team. The thought did offer some advantages though; when Rodney let out a sound, Sheppard had been alerted that there was potential trouble ahead.

"Heeeeeeeey. Look at that!" McKay rose from his crouch that permitted him to play in the control panel a foot above the floor. In his hands was a cube. An Ancient cube.

"What is it?"

"Don't know, but it's emitting energy. A lot of energy."

"How much is a lot?"

"You know what I'm going to answer to that, why don't you stop asking?"

"How much is a lot?"

"Lots and lots," Ronon answered for Rodney.

"Right you are, my muscled friend." McKay smiled fondly at the box he was holding. "I've got what I came here for, namely, new technology, so, shall we go?"

"We still have three rooms to check out."

"Get to it! I've got work to do!" McKay replaced the section of the wall he had dismantled in his quest for power.

Ronon and Teyla moved out, leaving Sheppard to guard the scientist. "What do you think the cube does?" They had found it in a secret compartment, which led Sheppard to wonder why the Ancients always had to be so sneaky.

"Hmm? Oh. Don't know .Yet. Much too early to tell. Got to run some tests." Rodney was happy and smiling. He knew something.

"You have an idea."

"Ah, yes. An idea. One that I have to verify." McKay put the cube in his pack and shouldered the black nylon bulk.

The men exited the room and headed off to the next one. Ronon and Teyla were flanking the door, listening to Rodney's avoiding responses.

"But you have an idea," Sheppard insisted.

"I've seen something similar in the database." Rodney indicated the door impatiently.

Sheppard momentarily desisted. He would go visit the lab tonight, before heading off to bed. McKay would have more information by that time, and be tired, so loose at the tongue. Decision reached, he stepped up to the door and opened it.


	2. Chapter 2

**Chapter 2: I should have known better**

In the car, the radio stays silent. John will not risk another reminder. This week has been difficult enough, this day will be enough of a trial, he doesn't need to reinforce it with another shot of musical battering. With his luck, he would fall on a R.E.M special. He snorts. John Sheppard: still alive to see the songs that have marked his life turn into golden oldies. Who would've thought?

The car purrs, but John feels none of the thrill and satisfaction he usually does. It won't be a pleasant trip, it will be a horrible day, a distressing weekend, he knows. He knows because he already feels the anguish.

What is he going to say? What is he going to do?

He pulls to the side and shuts the engine before reaching the end of his road.

"Pull it together, John," he pleads with himself, closing his eyes, breathing deeply. He mentally reviews his luggage, but a forgotten item is not the problem.

He had almost managed to outrun it, but when the phone rang and that voice reached out to him, in that familiar speech pattern. The name, the request, the same that comes through the mail every year.

It was a phone call, this year, or rather, phone _calls_. He couldn't refuse, but he couldn't accept. He stayed silent for a long time, listening to the breathing at the other end of the line. He clung to that touch of life, and finally decided that he wanted it. Needed it, perhaps. Some familiarity in a life that has been foreign to him for longer than he cares to recall.

Yes, he said. One word, and it brought him here, in his car, on his street, squeezing his eyes shut tightly because he has carried this weight a long time. It is so heavy, he cannot stand straight anymore.

**O-O-O-O-O**

The nights in Atlantis were seldom quiet. That night, without impending doom, a freshly resolved crisis or the Wraith on their merry way, Atlantis was quiet. Quiet in the way office buildings could be, after hours, and of course, that was it; that section of the city was the industrial section. Sometimes, Sheppard forgot how big, how impressive and imposing Atlantis was.

He was so at ease, everywhere he went felt welcoming and warm, that he found the concept difficult to grasp. It was home, not some soulless collection of rooms and corridors.

Sheppard's boots made a loud thump, thump as he walked with the heavy feet of a man ready for bed. The lights dimmed at his approach, allowing for his burning eyes. He sometimes thought of the city as a doting grandmother, warm, smiling, the smell of molasses and tea never far behind. Weaker than she used to be, but with a knowledge and wisdom only years could bring. No matter where he went, Atlantis embraced his presence, showed him things he never could have known without her.

He reached the labs and the square of light that spilt from Rodney's space, leaning in the doorway, watching the scientist work on the cube he had found earlier. Quiet had settled here too; the labs were devoid of life but for the overlord himself. There was no one around for at least a mile; all had left work to go eagerly toward home. This was not an unfamiliar sight, for John. The hunched back, the empty coffee cup, the blue glow of a laptop and the whitish light of a desktop lamp amounted to McKay's late-night life.

"Hey!"

Flailing hands, a cup of coffee swept away, the blue glow of a laptop and the whitish light of a desktop lamp were McKay's late-night life once John appeared at the door. Grinning in satisfaction, Sheppard strolled across the lab and bent over to pick up the cup that had gone flying along with Rodney's hands, which were now clutching at the scientist's chest as he breathed, panting dramatically. Sheppard rolled his eyes, returned the cup to its previous location and leaned against the workstation.

"Don't _do_ that! You nearly gave me a heart attack! Where would you be if I died, hmm? In deep, that's where you'd be, in very deep."

"Come on, McKay, it's not like I jumped out and shouted." John held back the grin, because what he had done was exactly that. "What's with the cube?"

McKay glared half-heartedly and mumbled unflatteringly, already gearing up for a long-winded explanation.

Sheppard quickly cut in to stop the expository essay he could see looming in the near-future. "The cube. What does the cube do?"

Thrown off-course by the interruption, Rodney took a few seconds to reorient his speech. "Yes. The cube. It's what I thought it was. I knew I had seen it in the database."

"Rodney," John said, sighing impatiently.

"It's a box." McKay looked at Sheppard the same way he looked at inbreeding natives, or what he perceived to be inbreeding natives.

"I can see it's a box. What does it _do_?"

"What does it do? It's a box. It holds things, inside."

"I know what a box's used for! Don't be a jerk."

Rodney smiled, amused and pleased by Sheppard's interest. He leaned in, catching the juvenile fever that followed John everywhere. "If I'm right – and there's no reason to think I'm not – this cube, this marvellous metal box holds…" Rodney paused for added drama. "…control crystals."

John visibly deflated. "Control crystals?" He looked at Rodney, disillusioned. This was not cool at all; he should have gone straight to bed. "They hid control crystals in the wall?"

Rodney was not done. His smile widened, his head nodded and he looked around the lab, as if expecting a surprise attack. Seeing the area was clear, he leaned in further. Sheppard leaned in too, intrigued despite himself.

"Yeah. Control crystals. For the index. They must've hidden it when they left."

"The index?"

"Yes!"

"What index?"

"The Ancient index!"

"There's no index!"

"There isn't right now, because the control crystals are in that box." McKay pointed to the shiny cube.

"An index of what?

"Of everything the Ancients have ever done. Everything in the database, listed neatly, accessible from the Chair. _Everything_." Rodney's eyes glowed and his mouth was curved in a happy little smile. He wanted it so much that John could hear the series of gimme-gimme-gimme-gimme running wild in Rodney's mind.

Sheppard whistled his admiration. "How come you never told me about this?"

"I wasn't sure…but now, finding the box. Look, it's all here." McKay typed a few keys on his laptop and presented his world to Sheppard. Diagrams, texts and images piled unto the screen, all depicting the cube. McKay continued with his explanation, "This here is a diagram of the cube. See how it looks smooth on the outside? It's not; when you touch it, you can feel a pattern. It's made of tiny interlocking squares. They all need to be activated one by one for the cube to split, but problem is they each have an access code. Without the access code, they don't budge." McKay indicated an amount of text. "That's all I've found so far to break the code. It's really…advanced. I'll get it, but…we might not have the index for a while, with the roof continually threatening to fall on our heads and me taking the place of a support beam."

"Well, you've got the bulk for it, anyways." Sheppard smiled, softening the blow.

"And I've got the brains for this. I've got everything, it's a wonder I don't have a fan club."

"The Rodney McKay Fan Club, where IQ and ego abound."

Rodney huffed, but his attention had returned to the laptop screen. The mystery of the day had grabbed him, leaving nothing for the mortal world. It was all about the cube now, and Sheppard knew when to take his leave. He landed a solid hand on Rodney's left shoulder as he advised him not to linger. "It's already midnight, don't stay up too long."

With a vague motion of the hand, McKay indicated his awareness of someone speaking and demanded that he shut up. Sheppard slapped McKay's back, hard, before heading off, letting the darkness and quietness of the night escort him to his quarters.


	3. Chapter 3

**Chapter 3: Long, long, long**

Five hours on the road in complete silence does not allow for the emptying of one's mind. John will brave the airwaves. He turns the dial and is forced to laugh because the Beatles are there to pick the wound again.

_But still they lead me back to the long winding road  
You left me standing here a long, long time ago  
Don't leave me waiting here, lead me to your door._

He contemplates the straight road ahead. Another hour and he will be at the border. Then it will be three hours up, up, up in the true north strong and free.

He is not ready, and does not think he will ever be. The voice of the midday presenter is bright and cheery. The Long and Winding Road, our Beatles track to start the hour, she says, and reminds him that fifty years ago today the band ceased to play.

April tenth, the presenter says, is a day that will be remembered as one of great loss for the music world.

John cringes.

In his car, with the road and deceased musicians as sole company, Sheppard thinks that April tenth will have a new meaning soon.

He switches off the classic rock station he usually enjoys. The past is alive enough today, he doesn't need it shoved down his ear canal.

**O-O-O-O-O**

Glad his schedule would be cleared of the night patrol for another two weeks, Sheppard checked his watch and decided on a last circuit. In an hour, he would be relieved and able to get some sleep, enjoy his day off in peace. The colonel had nearly reached the midpoint of his circuit through the section that housed quarters when the lockdown alarms blared through the city. He cursed for the day off that would not be, and activated his radio while running and getting his sidearm out of its holster.

"McKay!" he radioed, having seen the man exit his quarters twenty minutes earlier.

"I know; I'm on it."

"Where are you?"

"Chair room."

"Obviously, where else have you been these past weeks."

Satisfied that the Head Geek was on the case, Sheppard continued to run hoping to make it to the corridor adjacent to the control room before the city shut down completely. He stopped running at the door that separated the section holding his living quarters and the next.

"Damn it," he said, thwarted in his efforts. He ran his hand over the control panel, but the door refused to budge. He retraced his steps to the transporter, trying to raise Elizabeth. She answered the third time he spoke her name.

"John, control room reports the whole city is under lockdown."

"McKay's checking it out; he was working on his new toy, he's in the Chair room. Where are you?"

"In my quarters. His new toy?"

"The index."

"Right, yes, he told me he was exploring the database this week. Where are you?"

"I'm in the corridor of Living Section Three. The doors are shut, transporter's not going anywhere." He left his hand on the control panel and demanded that Atlantis open the door for him. She did not.

"It's the whole city," Elizabeth said, her voice calm.

"I've got patrols out. I'll see what they say."

"I'll contact Rodney."

"Sheppard out."

John spoke with the marines on patrol, and once they all had been contacted, he moved on to the people that were most likely in their quarters. Lorne answered, confirmed his position, as did Zelenka, and many others that were on the other side of the doors lining the hall. Carson was in the infirmary, Teyla in her quarters and Ronon was roaming the walkway, having gone for a run a few minutes before the lockdown. Left without scintillating conversation, John grew restless, and seeking a timeframe for his incarceration, he contacted the scientist in charge. "Hey, McKay, how's it going?"

"It's bad, Sheppard, bad, bad, bad. The city is in lockdown or had you not noticed?"

"So, you got nothing?"

"It's been five minutes!"

Sheppard was comforted by the sound of Rodney's low-level-panicky tone; it was normal, things were under control. "Five minutes! You're slipping there, McKay."

"Shut up and let me work. Don't call me, I'll call you."

Walking up and down the corridor was profoundly tiresome, John later realised, so he began harassing people. He checked in with the no-longer-patrolling marines, with Elizabeth and Rodney. He bothered Teyla, Ronon, Lorne, Carson, and Sergeant Williams in the control room.

Eventually, he settled down, back against the door, and proceeded to pester Lieutenant Cadman who was on the other side and always up for a chat. He regularly felt the pulse of the city's inhabitant through the only marine who did not see him as CO every single minute of every single day. He believed her attitude had to do with her stint in McKay's head – she had seen John through Rodney's eyes – but he would not stake his life on it. It could very well be that she was more discerning than most, or less respectful. Either way, he was glad to have something to do, for his uselessness was intolerable.

He hated not being involved in crises, and checked in with Rodney more often than he should, getting aggravation and insults in return for his concern. At first, the normality of the response was encouraging.

When the third hour of lockdown came around, Sheppard found his confidence waning. "McKay."

Silence.

"McKay."

More silence.

"Rodney!"

"Roooooodney."

"WHAT!"

"What's up?"

"I. Am. Working!"

"What's going on?"

"Did you not listen? I. Am. WORKING!"

Sheppard's hope for a quick and painless resolve of the situation was trumped by the aggressiveness of Rodney's tone. Choosing optimism regardless of what reality suggested, John answered, "Yes. How is that _going_?"

"I can't access Atlantis' main control because, oh, look at that, we're in lockdown, and Atlantis' wonder boy keeps interrupting my work. How do you think it's going?"

"So, check in later?"

"Get off your radio. You're nothing but a nuisance! We have no use for you."

Reeling from the unusual virulence of McKay's retort, Sheppard called Elizabeth, who told him nothing new, a bored Lorne, and Zelenka, who knew even less than he did. He then checked in with Teyla, who was taking the time to stretch, 'as should you, John, this is a perfect opportunity to try those exercises I recommended,' and Ronon, who was lazying at the highest point of the walkway and more than eager to entertain and be entertained.

When the conversation with Ronon had been extended as much as it would sustain, Sheppard rose from the floor and started stretching. This inaction incensed him. The uselessness he felt, the time wasted, sitting here and waiting. He hated that Rodney had to work alone, but was glad most of the population of Atlantis was in their quarters, as any sane person would be in the first hours of morning. Looking at his watch, John realised they were in their fifth hour of lockdown and decided to check-in with the controller of it all.

"Rodney?" he asked, mindful of Rodney's state of mind. Pressure was good for the scientist, but hours into a crisis he had to handle alone would not put him in the sunniest of dispositions.

"What? Sheppard, seriously, WHAT!"

Sheppard was glad he had called, McKay seemed like he was cracking under the pressure. It surprised John, for in an emergency McKay had his moments, but he could generally stay calm as long as he had work on which to concentrate. "How're things?"

"Are the doors open? Hmm? Are the damn doors open?"

"No, they're not open. Yet," he said, trying to infuse some of his confidence in the last word. McKay would have fixed this and be gloating soon enough.

"How perceptive. Good for you. Get off the damn radio."

"What you doing now?"

A short, impatient sigh preceded Rodney's answer. "Eating a powerbar."

"Aaaand?"

"Trying to open up a path from the Chair room to the control room.

"How far you got left to open?"

"From the Chair room to the control room."

"Ah. Listen, you can do it." Sheppard was ashamed of the doubtful tone of his voice. He did not even believe himself.

There was a moment of silence before McKay answered. "Nice. Are we done here? Not that I don't appreciate the pep talk, but I have things to do. Important things, Sheppard, can you understand that? Do you get that the world does not revolve around you and your magic gene, that other people, depsite their artificial key to the city, can contribute!?"

The click in his ear told John an answer was neither needed, nor wanted.

When the seventh hour of lockdown came to be, Sheppard was listening to the chatter on the public channels, growing increasingly annoyed by his inactivity. He allowed the voices to lull him into a semi-resting state, but was disturbed from his rest by the city shutting down completely before surging back to life. A strong pulsation followed the city's return to power. It came from everywhere, like a strong wind, a pulsing wave that engulfed him. He got up and moved through the corridor, trying to pinpoint its provenance. Every door he passed vibrated with an insidious force. He knocked, but no one answered. He returned to stand before the transporter door, hands on hips, a puzzled frown marring his features.

The wave intensified, pressing on him from above, below, right, left. He felt the resistance his skin gave, and moved through his prison in an attempt to evade the heavy pervasiveness that threatened to overwhelm him.

He walked his limited perimeter once. It did not calm him, or minimize the effect of this wrongness flowing through the city. It pressed down on him with an intensity that hovered on the edge of pain. Each breath was hindered, each heartbeat a painful twinge; John was certain he could feel his blood travel sluggishly through his veins as if carrying the wave through him. He was intensely uncomfortable, as if his skin was suddenly too big and too small, floating on his muscles and tightening agonizingly. "Lieutenant?" he shouted over the white noise that superseded all other sounds. He pounded his fist on the door, but Cadman remained silent so he moved on. One door after the other presented only stubborn muteness and John's discomfort grew. Wrong, this was wrong in a way he could not explain. He felt it all around him, trying to get inside. He felt it inside, trying to get out. It surrounded him, trying to take him apart, and intensified rapidly. A sudden and violent headache made him close his eyes and fight for breath; a strong nausea forced his stomach to empty, and once it had done so, John collapsed to the floor, panting, certain his brain was about to pound its way out of his head. When, finally, the wave washing through the city retreated, he lay on the ground, drained. Forcing himself back from what he had thought was approaching death, John sought one voice.

"Rodney!"

He demanded an answer repeatedly, but there was none. Infuriated by Rodney's inaccessibility, John tried to reach someone who was close, not ignoring him from across the city. Every door received a harsher treatment than its predecessor. John wanted an answer and concentrated all his strenght on obtaining it. He needed for just one voice to be heard, for just one person to acknowledge him. By the last door, John had moved on to violent kicks and body slams; nothing changed, no one moved, no one spoke to him. The rushing sound gave way to another: silence. He raised a hand to his earpiece and appealed for solace.

"Teyla?"

He waited. His heart beat, loudly. He felt it, heard it, pumping blood and fear through his body.

"Teyla. This is Sheppard. Come in, Teyla."

He waited; his pace quickened. His hands formed fists at his side.

"Teyla, are you there?"

When she did not answer, he sought another source of reassurance. "Ronon."

The quiet baritone he wanted so much to hear did not sound out through the radio. He called, again and again, with increasing volume and trepidation, but there was nothing, only silence and cold.

He persistently tried to hail his team before moving on to Lorne, Zelenka, Elizabeth. The patrol teams had fallen quiet, and John was about to call Carson when Sergeant Williams, the gate technician, hailed him.

John answered with feigned confidence, pushing distress away. "Sheppard. What's your progress?"

"Nil. There's just me. All the others, they - I don't know what happened, sir, there was something, like power, and they…they keeled over, sir, and died. Sir. I couldn't reach you."

"It's alright, Sergeant, I felt it too." Click, click, click, pieces fell into place. A pulse, a lack of response, a confirmation. John squeezed his eyes shut, tightly. Images of people, his people, ran through his mind, all accompanied by a glaring neon light pronouncing them dead, as Williams' colleagues were. Elizabeth's amused look, Teyla's calm acceptance, Ronon's reassuring strength, Rodney's vibrancy. Zelenka's sharp mind, Lorne's loyalty, Cadman's smirk. The usual questions, how, why, who, longed to be answered, but Sheppard ignored them, wanting to free those that remained before understanding what had happened to them all.

"Sir,' William said softly, questioningly. His vocabulary was limited; thought-process hindered by the sight of his colleagues - friends - lying by their chairs, frozen in death. He had not been able to reach Doctor Weir. He had thought for a distressing minute that he was alone in this great city.

John understood the plea and chose to unburden the young Sergeant, as was his duty as commander. "Monitor the situation. Contact me if there's any progress, I'll be here. You'll be fine, we'll work this out."

"Yes, sir."

"Sheppard out."

John called Carson and received the same kind of bewildered answer.

"Carson?"

"Dear Lord. They're all - they're all dead," Carson said softly.

"All?"

"What happened?"

"You felt it. The pulse?" John could not believe he and the Sergeant were the only one who had felt the earlier disturbance.

"Yeah. I was taking a moment to rest, it woke me. Pressure, blinding headache one minute, then the next it was gone. What was that?"

"I don't know, haven't been able to reach Rodney."

"This cannot be happening. My nurses, my patients. I'm the only one left."

"Listen, just, do what you can, we'll get this sorted. Williams is in the control room and I'll go citywide, see who answers."

"Williams. He's a gate technician, can he get us out of this? He's no Rodney, we can't expect –"

"We'll get out of this, Carson. Just prepare the infirmary to receive any injured."

Carson set to a task, John stopped pacing the corridor, rested his forehead against the transporter door and struck the unyielding metal with his fist. He kicked it, slammed himself against it. He attempted to make it bind, to make it move; he wanted to be away from here, to have never come to this forsaken galaxy, this greedy city. He hit, kicked and abused the doors that trapped him. Guttural moans escaped him; a primal fury took over, a basic fear.

He stopped suddenly, breathing heavily, sweating through his shirt. Cold was catching up to him despite his agitation and Sheppard wondered how it was that he had never noticed the chill that resided in the corridors. He had always felt very comfortable strolling in the halls of Atlantis, but had never been trapped in them before. Sweat dried quickly and prickled his skin. He kicked the door once more before turning and resting his back against its solidity. John sank slowly to the cold floor. His knees supported his elbow, his hands received his head too heavy to hold up, and he sat, uncomfortably chilled, for long minutes before the environment cooled his temper. He raised a hand to his earpiece.

His voice broadcasted throughout the city by way of radios. "This is Colonel Sheppard. If you hear this, please contact Sergeant Williams in the control room. Contact the control room, immediately."

Sergeant Williams reported within minutes. Beckett, Levin, Latour, Kusinagi, Miller, Williams and Sheppard were the names he read out to John. There were three scientists, two sergeants, one lieutenant and one doctor left under his command. John hoped there were more, that they did not answer the hails because they had misplaced their radio, or fallen asleep. He hoped, but doubted. In the middle of such a situation, people were alert in their quarters. Quarters through which a wave had rushed, a wind had flown.

Skeleton crew was all that was left. John felt it in his bones.

Sheppard ran both hands over his face. He closed his eyes and sighed. This was killing him. So many, gone, and all he had done was pace and pound the doors.

"Did it!"

Rodney's voice made Sheppard jump. "Rodney! Damn it! Where the hell have you been!?" Anger returned, quickly coating the surge of relief hearing that particular voice had brought.

"Are you kidding me? Where have I been! I've been in the Chair room!"

"Why didn't you answer! Why didn't you call the control room! I told everyone to call Williams! That included you!"

"I took off my radio; you were getting on my last nerve! Now, city's letting me in, control room reports the same. You should be able to activate the transporter."

"How?" The quick change of mood Rodney exhibited was jarring, but not particularly new.

"Just step in and press, Sheppard, you've used them before. Meet you in the control room? I'll let Elizabeth know."

The mention of Elizabeth made Sheppard forget his annoyance at Rodney's evasiveness, and his sharp intake of breath sent Rodney into panic mode. "What? What, what, what? What happened, what have you done?"

"I haven't been able to reach Elizabeth for hours."

"Well, she's probably just fallen asleep. I can't get Zelenka either, lazy quitters!"

"There was a pulse, wind, earlier, you didn't feel that? I sure thought I was done for. I can't confirm, but –"

"What - what are you saying?"

"I'll just check it out, ok? Go to the control room, I'll meet you there." Sheppard refused to voice what he knew to be true until he could verify it.

"Right…"

"Just go, I won't be long. Oh, hey, no, stop by the infirmary, get Carson, then go to the control room. I'll go city-wide, tell everyone at once and meet you there."

"Ok."

"Sheppard out." He keyed his radio and selected the emergency channel that would patch him through every person that carried one. "This is Colonel Sheppard. The city is no longer under lockdown. I repeat, the city is no longer under lockdown. Everyone rendezvous in the gate room immediately. Gate room. Immediately."

He stood in front of his door, hand hovering over the controls. He moved to the left, plastered himself against the wall and activated the controls. The following moment was anti-climatic; John stepped into his room to find it as he had left it before his shift, thought slightly colder. He exited and opened the door next to his, then the next one, the next one, the next one. He did not need to step in after the fourth one, for he knew what he would find. He went to stand before Teyla's quarters, breathed in deeply and triggered the door. The air was cold here too, and Teyla was as most of the others he had found: lying in a heap on the floor, completely still. John walked over, crouched beside her and foolishly felt for a pulse. It was not there. He placed gentle fingers upon her eyelids and hid the lack of intelligent light and life that left only emptiness in her eyes. He lingered a moment, running the back of his fingers over a cold, still cheek.

He straightened, but could not leave. The floor was not the right place for a friend to lie, and he had a request to honour. Crouching down, he slipped his arms under Teyla, lifted her as he straightened once more and gently deposited her on her bed. Rigor Mortis had yet to set in, so he arranged her limbs in what would be a comfortable position, if she was only sleeping. He settled the blanket that lay at the foot of the bed over her cold, lifeless body. Touching his forehead to hers, he closed his eyes and spoke the words she had entrusted to him were she ever to meet her demise away from her people. "Teyla Emmagan, daughter of Tagan, honourable and loved, I, John Sheppard, commend your spirit to eternal peace."

She would be safe, she had said, from all that would seek to take her spirit from its rightful place, was a trusted friend there to commend it. John had grudgingly accepted the responsibility, as Ronon and Rodney had done. Always unwilling to face his people's death, he was pressed against the face of death, warmth from his skin seeping into that of a lost friend. He moved away from her, breathing in deeply, fighting to loosen the tight hold sorrow had over his heart.

Wanting to go and see to Ronon, to Elizabeth, to everyone, but untrusting of the transporters, John instead took the long way to the control room. When he entered the room, he saw that the worst scenario was as horrific as he had imagined. His count had been correct. He looked at the beseeching eyes that stared at him. Some were filled with tears and others with dismay, but all looked to him for guidance. The bodies of the control room crew had been moved out of sight of their position, for which John was grateful. He needed a moment to reintegrate his role of Lieutenant Colonel John Sheppard, commander of the Atlantis base. He needed a moment to chase away misery.

McKay stood at the screen that depicted the city and its life-signs, arms crossed in a solitary hug. All the dots were in the gate room, all eight of them. As John stepped closer, Rodney turned to face him, his blue eyes drowning in horror. He said, "I think the sensors are offline. They must be."

Sheppard could not lie to him, nor would he wish to. "Doubtful. I went to Teyla's room. She's…she's dead." He turned to the rest of the frightened faces, feeling McKay's eyes burn a hole through his back. He wanted to say more, explain to Rodney, and grieve for just a moment, but Beckett, Levin, Miller, Williams, Kusinagi and Latour waited for John to take command. He resisted the urge to offer his usual platitude.

Everything would _not_ be fine.

The infirmary became temporary quarters for them all. It was the practical that grounded Sheppard, thinking of what needed to be done rather than what had happened. Carson took charge, supervising the rearrangement of his domain from infirmary to communal room.

When they were settled, when Sheppard had done his duty, spoken and reassured as Elizabeth would, he returned to the control room, to Rodney.

Hunched over his laptop, Rodney typed and frowned.

"Anything?"

"Everything's on, but the most important systems such as the gate, the database, the Chair, and the shield are inaccessible. They're still locked from us." Rodney reclined, seemingly pleased with himself despite the limited access to major systems.

"Can you make the quarters colder?" Sheppard kept his tone flat.

The satisfied look fell and Rodney looked at John imploringly, as if he could take it back, could make it go away. He could not; asking Rodney to turn the used living sections into a morgue had to be done. No one wanted bodies that had begun to…Sheppard let go of that train of thought quickly. "Rodney. Can you make the quarters cold?"

The scientist nodded, typed a few keys and stilled.

"At least we can still live here," John pointed out, after a lengthy silence, "provided the city doesn't go into lockdown again." His tone was too light, too casual. It was pointless to be bluffing his way through this, but necessary. "Any idea what caused this?"

Rodney stiffened and stopped typing, but did not look at John. "Not sure. The pulse? I think it might've been a conditioned response, the systems are old, a bug, malfunction was inevitable." Rodney paused before asking, his voice rusty, "How many?"

"Eight, total." John did not even try to pretend he had misunderstood the question.

A sharp intake of breath and Rodney nodded. "Right." He stared at his screen, rested his hands on the keyboard.

Sheppard hated Rodney's quiet acceptance. It was just one more unsettling thing in a list that was growing too long.

He breathed in deeply. Things had to be done, right now. Allowing himself a rare moment of vulnerability, John dropped a hand on Rodney's shoulder and squeezed. Warm skin moved under his fingers, under the shirt against his palm, assuring him that life was there to stay. He let go and walked away quickly.

They would get through this, but he could not be assured they would all be unharmed once they did.


	4. Chapter 4

**Chapter 4: The long and winding road**

It's raining in British Columbia. Heavily.

This makes it difficult for a driver to read the names on the street signs. John slows down at each intersection. No one is following him, and he takes that as a positive sign. Maybe his day won't be as bad as he thinks.

It could even be fun, nice. Snorting, John doesn't allow delusions to take a firm hold on him. Nice. Right. This is so far from nice it's about to come around the other side and bite nice in the ass.

With a jolt, John recognises the street name and turns left, as he was instructed to do.

He should have refused, been enraged by her call, by the intrusion in his life. In truth, he had been guilt-ridden, so deeply ashamed and impossibly cowed when her strong voice reached his ear. At first, he was taken aback, wondering why she was calling, why she pushed further this year, when he had made it clear to everyone that he had no wish to see them or to be included in their plans. He wanted a quiet life, far away from people and potentially soul-destroying situations.

She had gotten his number easily, she taunted. She was angry, told him he was a selfish bastard, that he had no right to act as he did. This was an important day, she said, get out of that self-pitying slump you've been in for the last ten years and be who you were.

"_I don't know you,"_ she said, venom in her voice, _"but I know everyone else has come at least once. You're the only one hiding!"_

You don't understand, he said coldly, before slamming the phone down. She called, again. Again. Again. For days, the phone rang every few hours. Rings that broke the silence in the house. Rings that cut into John, forced him to sit at the kitchen table and stare at the phone until it stopped its infernal racket.

Finally, on the seventh day, he picked up the receiver and said yes. Now here he is, on a street far from his own. Large houses, perfectly kept lawns, window boxes, shutters: suburbia at its best.

He does not need to check the numbers on the mailboxes, though he does. The house is the last one on the street, a bit removed, encircled by massive trees. There are cars filling the semi-circular driveway. The street is a dead-end, it's the only reason John does not drive on, but turns into the driveway

"Pull it together, John." He whispers the new motto to himself before turning off the engine. The plick-plick-plick of the rain on the car is the only distraction he finds, and he listens to it.

The day mirrors John's state so perfectly. Heavy skies, sombre atmosphere, rain. This is me, he thinks, as the front door of the big white house opens. This is me: an undesired storm on a special day.

He sees Jeanie, in the door. Recognises her though she, like him, like them all, has aged. Her hand is raised in greeting. She is smiling.

Breathing deeply, he puts on his John-Sheppard-charming-man mask and steps out of the car. As he stands, he feels the crystal dig into his flesh through the material of his pocket. An upsetting reminder.

The rain is cold on his skin, but he does not hurry to the protection of the porch. He would rather stand in the rain than walk in that house, but at this point, changing his mind is no longer an option.

**O-O-O-O-O**

It seemed strange for the sun to be high in the sky, for a gentle breeze to carry the mingled scents of the earth, the flowers and the ocean to them. It was almost indecent for the Mainland to be so beautiful.

John felt the sky should have been heavy with black clouds and rumbling thunder, the wind biting and sharp. For this day to be so comfortable, so utterly pleasant, felt like betrayal.

He stood closest to the water, on the far left of the cemetery. Straight, orderly rows of graves stretched before him, all marked by personal items the dead had cherished, or the survivor thought they had cherished. Hands on hips he surveyed the horizon, eyes high above the ground, ignoring the mounds that covered the ground. Halling would recite his prayers soon, there would be tea and tears, and then they would return to the city and John would put all of those that were gone behind him.

He wished it were so easy.

His gaze flitted over his people. Levin, Miller and Williams were standing by different graves. John supposed those were people they had been closer to: friends, teammates. Latour and Miko were assisting Halling in his preparation, wiping a stray tear when they stopped moving for too long. Carson was walking along the rows, stopping here and there, crouching, reaching out to stroke the earth. He too, wiped his eyes with the back of his hand. Rodney stood at the opposite end of the graveyard, starring straight ahead.

John frowned. Something glinted in McKay's hand. The crystal. He had taken the crystal here and was toying with it. John eyed the scientist and noticed his dishevelled appearance. All the others had taken care to dress in clean, pressed clothes, but Rodney looked like a man who had just returned from a three-day bender.

The surge of irrational anger was quickly quelled. Everyone had a certain way to deal with loss; if Rodney wanted to give up on hygiene and personal appearance for a while, that was his prerogative. John would only step in if it endangered anyone, but he believed Carson would comment long before John was forced to: health concerns and all that were the doctor's main area of control, after all.

Eyes following thought, John's gaze settled on Carson who was walking slowly toward him. He watched him approach, unmoving. Waiting.

"It's a beautiful day," Carson remarked. "Glad we could send them off under the sun like this."

John snorted.

Carson turned to look at him. "Small comforts are important, John."

"I know." He did not care. There was no comfort to be had anymore. Only the bitterness of failure, the hopelessness of loss.

They stood silently for a few minutes. John watched Rodney walk away from the gravesite. He seemed to be talking to himself and that almost made John smile. It was familiar.

"I'm worried about him," Carson said, having followed Rodney's path.

"He's fine. It was a big shock to everyone."

"From two-hundred and seventy-nine to eight. Seven with a natural gene, one without."

John frowned. "I guess we were lucky," he said, and had to restrain the laughter that rose.

"Good Rodney was in the Chair room, isn't it? Only surviving artificial gene carrier. Don't know what we'd do without him, if there was another lockdown." Carson's tone was neutral, his words carefully pronounced.

John turned to Carson. "You might want to think twice about what you're implying, _Doctor_."

"Stating facts, _Colonel_."

John refrained from answering, hearing the bite in Carson's tone. John deserved it, he had bitten first, but Carson voicing the thoughts that John tried so hard to push away was another checkmark in the unsettling column.

Carson eventually sighed and moved away, returning to his visits of the graves.

The questions he had raised stayed with John and they displeased him greatly. He was unable to ignore them now that another had expressed the thoughts he considered paranoid.

Rodney had not returned from his walk when the celebration of the souls ended. John found him sitting under a tree, talking to himself and stroking the crystal.

* * *

TBC... 


	5. Chapter 5

**Chapter 5: She said, she said**

She's hugging me, John thinks numbly. Why is she hugging me?

Hugging him and telling him she is happy to see him, she was worried, they were all worried. They had begun to think he would not come.

Jeanie releases him after he awkwardly pats her on the back, and she turns to the door. She puts a hand on the handle, but does not push the door open. "We're all glad you came. It's been hard, not knowing for so long. I tried to find you, to ask you, but for years you were on the move and the Air Force wouldn't say a word. The minute you retired, I pounced on it. No one could tell me. I've wanted to know what happened, and now…you're here, and I'll be able to get the remaining answers."

She is no longer smiling. Like the rain, John will make everything lose its lustre. "I received your letters," he offers, knowing it isn't the right thing to say because he never answered them.

Jeanie releases the door handle and moves toward him, returns to the hugging. Her voice is soft in his ear. "I'm glad you're here, John. You don't know what it means to us."

This is the part where John tells her he's happy too, the part where he confesses, as convincingly as he can, that he's glad he came too. Enclosing her in the circle of his arms, he cannot lie. "I'm sorry," he whispers intensely. "I'm sorry." Jeanie has to understand, he needs for her to understand.

"Don't be," she says, hugging him tighter, almost fiercely. "You don't have to be sorry. You're all here. This is a good day. It's a beautiful day."

John hears her halted breathing in his ear, fighting with the heavy splatter of the rain and the sound of his own heart, beating, beating, beating. The perfect day, she says while sobbing in his arms and getting wet from the cold rain because the wind has changed its path. He contemplates the cold, the rain, the crying.

"Yeah," he agrees, if only so she hears it.

**O-O-O-O-O**

Later, when the night was moonless and tranquil, John sat and contemplated the silence that only the steady snores from the bunks disturbed. Inner peace had not been achieved in so long, not since his first dance with death, the first vacant eyes he ever had to shut, but tonight the outside world was calm. He did not expect peace, either internal of external, only wanted to stop feeling this way. Hurt, afraid, stuck in a city that would not respond to him any longer. No database, no gate, no control whatsoever.

He had been happy, for some time. Content, satisfied, perhaps even fulfilled. Regardless of the Wraith, the Genii, the malfunctions and weather anomalies, he had been home. They had all been his people, she had been his city, and they could have done so much good, they could have erased the biggest blunder in history, vanquished the Wraith after having woken them. They could have freed this galaxy, of that he had no doubt, but it was all gone and only the Wraith remained. His amazing city, his extraordinary people: gone.

Gone just as Rodney would be, and if he thought John had not seen him slipping out of bed, he was insane.

"McKay."

The buck froze in the beam of the flashlight. He did not turn. John sighed and got up from his seat. The light showed him rounded shoulders, a lowered chin.

"Where' you going?"

The back straightened, the shoulders stiffened. "Washroom," Rodney said, tonelessly.

"Right." It was not far, not at all, just next door. Fifty-step roundtrip at most. John sat back down and turned the flashlight off. He heard the shuffle of Rodney's sock-clad feet growing fainter. John hated this paranoia, this mother-henning. Where are you? What are you doing? Where are you going? He needed to know. If he thought he could get away with it, he would tie everyone to his belt. Keep them close, follow a string when he needed to find them. They would always be there, at the end of the string. He would just have to tug, wait for them to tug and he would know they were still there. Alive enough to tug. One Tug to rule them all, One Tug to find them, One Tug to bring them all and in the darkness bind them. John liked the idea of a Ruling Tug and sniggered in appreciation. If only it didn't make him appear to be a completely hysterical _dork_, he would do it and explain it just like that.

Sighing, John closed his eyes and let his head fall against the wall. He was obsessing; it was not healthy, but seeing Rodney shuffle along, mumbling to himself, fingering that damn crystal he carried everywhere put John's failures in high relief. McKay had barely spoken to them today, was nowhere to be seen after breakfast. He had barely eaten, only worked. Chair room, Chair room, Chair room, that was where he spent his hours. He did not do anything. The Chair did not work, but he sat in it for hours, typing on his datapad once in a while. McKay was not the guy whom John thought would break like that. He had his moments of panic, but he always came through and carried on.

John sighed again. How did it come to this? Where did they go so wrong? Oh, no, there it was. The hurt. The overwhelming grief. So many. He bent forward, his hand fisting, his arms coming around himself, holding the misery inside. His eyes were shut tightly and he took particular notice of his breathing. In. Out. In. Out.

John saw their faces clearly in his mind. Those he knew well, those to which he smiled and nodded. His men, his scientists. Living here, taking possession of the most beautiful place in the universe. Curious, loyal, safe in the gentle cradle of the floating city.

Bent, John opened his eyes and turned his head toward the balcony. He needed to let this out. He could not keep pretending, being strong. He _needed_ it.

Rising, he pushed his chair back and went on the hunt for a balcony. He stepped out onto the first one he came across and leaned against the railing. His eyes were on the water that he barely saw, for the night darkened everything in its path. He did not see the waves, but he heard then, smelled them. He hated it, because she, too, was a danger.

He spoke quietly, a running commentary of pain, loss and imbalance. Invectives, curses, foul words he hoped the Ancients could hear. They had allowed this. They had done this to him; broken him, taken him to the edge and back only to leave him hanging there, fingers scrambling to hold on.

To hold on to what they had deigned to leave him. He had not done this; it was not his fault, but perhaps, if he had not joined the expedition, if he had not woken the Wraith. If he had not been misguided all his life.

After long minutes, John realised that foul words did not help anyone. It did not feel good, it was not freeing, but he cursed one more time before letting his hands wrap around the railing, his arms flex, his back stretch, his eyes close.

"Good?" Carson asked from behind.

Startled, John spun around, but did not answer.

"Feeling better?"

John shook his head. "Is McKay back?"

Carson shook his head in answer and John straightened, trailing a gentle finger on the railing, out of habit. "I'll go look for him."

"I'll come with you."

"No, you go back to bed."

"Nobody expects you to be a rock, John. You don't have to be the lonely leader." Carson paused. "Shall we?" he added, when all John did was shuffle awkwardly and rub a hand over the back of his head.

"After you."

Unsurprisingly, Rodney was not in the washroom. Even less surprising, he was in the Chair room. What was quite surprising was that he was _in _the Chair, the reclined Chair.

"I thought Rodney said the major systems were down…" Carson said, frowning. "The gate? The Chair? The database?"

"He did." John approached the Chair and put a hand on Rodney's shoulder. "Rodney! What the hell do you think you're doing?"

Rodney jerked; the Chair straightened and deposited him on the ground. He blinked vacantly for a moment or two, but quickly regained his sharp wit. Standing, brushing invisible dirt from his clothes, Rodney frowned at John. He opened his mouth to speak, but for once was too slow.

"What's this?!"

Rodney blinked slowly, but did not answer.

"Since when does the Chair work? I thought it was down!"

Rodney's face crumbled and it was too wrong. John stepped forward and Rodney stepped back.

"It isn't."

John froze, brain short-circuited by Rodney's quiet admission. He felt Carson move past him, heard the soothing burr asking what he should be saying. "You've fixed it."

"It was never broken," Rodney said, sending a resentful glare toward the Chair. He then sighed and his shoulders slumped, his back curled and his eyes locked on the floor. "It was never broken; she just had more control than me."

"Not broken? What do you mean!" Carson said, frowning concernedly. He glanced at John who had not moved from his dumbfounded stillness.

"I didn't mean to let her. It's her job and she does it well. Better than I can do mine."

"Didn't mean to what?" John finally asked, his voice cold and hard.

"She said it would cleanse the city; protect it. I didn't know. Then I tried to stop it, but…I wasn't quick enough."

John stepped forward, grabbed Rodney's arms in a too-tight grip and jostled him. "Quick enough for what, McKay!"

"I didn't know that's what she meant. By the time I realised it, it was too late, she'd taken control and left me in the dark. Us, in the dark. All of us…" Rodney trailed off, folded further into himself.

"Rodney. What have you done?" Carson asked, clearly confused, perhaps denying what he was hearing.

"It wasn't me! It was her! I couldn't stop it!"

John tightened his grip, as it seemed to be the only thing holding Rodney upright. He wanted to let go, watch the man fall to the floor. "Who are you talking about," he spat out, choosing to be angry because it was so much easier.

"Lyhal."

"Who's Lyhal?"

The crystal was held up before John's eyes. "Lyhal. We found her, remember, a few weeks ago, in the box."

"The index?"

Rodney nodded, then shook his head, then nodded again. "It's an AI, not an index. She's the city's watchdog. She primarily functions as an index, but when the city is threatened, she steps up, takes control and fixes it. This limits the strain on the city's system and protects them from unwanted access. Problem is she sees us as having invaded, us, without the natural gene, not you, Carson, Miko, Williams, Levin, Latour and Miller. She doesn't like us, me, we're not like you. She tolerates me. I'm still here because I was in the Chair and facilitated the lockdown. "

"You don't have a natural gene, you should've died too," Carson stated equally, as if it was a simple fact.

Rodney nodded. John tightened his grip, aware that it was hurting Rodney. "You did this."

"No," Rodney said, easing John's tension slightly. "It was her. She needed organic matter to interface with the city. She's embedded in the Chair systems, and I suppose she recognised my genetic makeup. Whatever the reason, she knew I was there and she showed me what I wanted. If you could've seen it. Everything is there."

Tension was back in full-force, bringing along fear, disbelief and horror. This was too much, pushing the limits of what John could endure. Year after year, he had moved on, walked it off, roughed it out, but this. Rodney had done this? Participated in their deaths? John could not believe that.

"And the pulse, was that," John swallowed the scream, "her too?"

"Yeah. She was trying to protect the city. It's what she'd been programmed to do. She just didn't like us, nothing personal, she couldn't like us. She likes you," Rodney said with a wistful smile, "she likes you a whole lot. She took great care to protect you during the lockdown. It made it harder for her because you were in the middle of it all, but you weren't hurt. Everyone was just fine after Carson fixed them up." Rodney smiled tightly at Carson who grimaced back.

"Why didn't you pull the crystal?" the doctor asked.

"I didn't know that she would kill them all. I thought she would…I don't know, fix the broken systems, or activate new ones. I saw threat neutralisation and went with it."

John let go of Rodney's arms. Oh, please, no. Not this. Not Rodney. John could not find the words. He was disgusted, appalled, but so sad. He looked at Carson whose face betrayed the same inner turmoil that was plaguing John. Forget about this, John ordered himself, the city works and there are things to be done. "Can we use the gate?"

"We can use everything. We could always use everything. I just…John. I wanted to find more, know more. There's nothing she can do, now. She wants you here, and she needs me. There's a reason I'm still here."

"You knew. You knew what was happening from the start. You lied to me, and you put us all in danger just to know more!" John turned away from Rodney, trying to calm himself, rein in the boiling fury that was threatening to burn them all. He saw the faces of the departed, transformed by anger and it was all he could do to keep his fists from pummelling Rodney. He did not want to hurt Rodney, but it would feel so good: Rodney had done this and John was going to be sick.

"No! No. You're all safe. She accepts you. If she didn't you would've all died along with the others. You're safe, every one of you. Nothing is going to happen. Look," Rodney said in his 'let's be reasonable' voice, "the more we learn about this place, the more chance we have of defeating the Wraith. We have the retrovirus. Granted it's not the best of plans, but it's the one we have, and one more than the Ancients ever had. We can do this. We can beat them. I just need more time! The AI will allow me to go through the database just like that," he enthused, snapping his fingers.

"Have you gone mad!" Carson exclaimed.

"More time with the AI that killed everyone in this city. You want more time with a murdering machine."

"It's just a crystal." Rodney sighed, stretched his hand out to John and let him see the crystal. When John moved for it, Rodney closed his hand and took a step back. "You know we can do this. You can do this, you have the strongest gene, I'm sure you just need to ask and she'll give you anything you want. Think about it! ZedPMs, location of other outposts, perhaps even other cities! Ships," Rodney almost yelled out, an excited grin to his face, "we could find more ships! You could have a whole fleet of them!"

John watched Rodney grow more animated, warning up to his sale pitch.

"Are you hearing yourself, Rodney," Carson said, coming closer to the man.

"Yes I am! You know we can do this. We can do this, get rid of the Wraith and preserve the city."

"No, I don't know that. Carson doesn't know that! Neither do you!"

"We can save everyone, how do you not see that!"

"YOU'VE ALREADY KILLED EVERYONE!"

Silence fell heavily over them. Carson watched, horror-stricken, but John had eyes only for Rodney, who backed away as if he had been hit. The surprise was short-lived, quickly replaced by the familiar righteous indignation. "I didn't! Lyhal was just doing her job; I was just doing my job! It was an error! A malfunction! It wasn't supposed to happen, but it did, and now you're just going to let it mean nothing? We could defeat the Wraith. You can't turn your back on that."

John turned away, fury and disgust battling for control. This had happened before and he had thought Rodney had learned something from the failure of the Arcturus project. He believed in Rodney, trusted him, and that made him a fool. "You don't want to go there, McKay. What you want to do is get the hell out of here, right now."

"But –"

"GET OUT!"

"Come along, Rodney. It's late, we should all get some sleep," Carson said, firmly, almost unkindly.

Standing motionless, John listened to Rodney argue as Carson pulled him away. He sat on the platform that held the Chair and refused to believe that Rodney had crossed the thin line between genius and madness.

He had to, but it was an excruciating thing to allow. Rodney making excuses for what was ultimately mass murder. Not his fault, he had said, just doing his job; a scientist trying to sell an idea, trying to entice with shiny ships and promises of victory.

Where had they gone so wrong?

John's eyes fell to the Chair and he heard Rodney's voice echo in his head: _I saw threat neutralisation and went with it._


	6. Chapter 6

**Chapter 6: Come together**

Walking into the house, being engulfed by the warmth and the sound seems to knock something inside John. He has been alone for too long, the sound and sight of people he knows overwhelms him momentarily, but Jeanie beckons him forward, into the living room where laughter flows.

It stops flowing abruptly when they enter. Jeanie takes her place beside her husband who sees her face, red with the cold and tears, and places a hand upon her arm. She nods, smiles and presses her hand to his. This is her perfect day. Her husband, John has forgotten his name, looks up and smiles at him.

John stands awkwardly in the doorway. Eyes are riveted to him. Some are still filled with merriment, but others are hiding beneath frowning brows.

One pair, clear blue, is warm. It rises with the owner and comes closer to John. Wrinkles mark the skin, white colours the hair, but the eyes are just the same. Friendly, filled with emotion, a little bit of home, a whole lot of past. Foreign. John offers a hand and his trademark smile in greeting.

The man pushes the hand away and John finds himself held, tight, tighter than he expected. "Don't be a fool, man. You don't shake hands on occasions like this."

John lets out a small laugh and returns the hug with slightly more willingness. "You know me and civilities."

"I'm afraid I don't anymore, but I can remember."

John is released, though hands stay on his upper arm, holding him, keeping him within arm's reach. He looks down into a kind and gentle face, and wonders why he ignored this man for so long. "Memory not the first to go, hey Doc?"

"Not for the important things." Carson has tears in his eyes, and his fingers are digging into John's skin almost painfully.

There is no way John is moving. Out of contact with them for so long, he only now realises how much he missed them. How much he has missed everyone over the years.

The world becomes a flurry of hugs and back-slaps, glad to see you's and how have you been's. Warmth, kinship, familiar. Home. Home. Home.

For a second, John felt as if he was crashing the party, but that second has melted away never to exist again. Stepping into the room might have been one of the hardest conscious choices he has ever made, but it offers such rewards that it now seems like the only path he could take. He has made some difficult choices in his life, but so rarely consciously that they blur into a mesh of instinct and duty.

Only one choice was ever this difficult, and even today, after all these years, he still hears Rodney's voice telling him that he had seen threat neutralisation and gone with it. That is what John did.

He remembers so well the day, the moment he decided what the best course of actions was.

**O-O-O-O-O**

The crystal was harder to take than John had thought. It had been three days since Rodney's admission, the Daedalus was due any day; John needed to act quickly. They could have walked through the gate, but John had needed time to think, to decide. He had offered, of course, but it seemed safer to them all to be transported by something that did not rely on the city's systems.

John walked through the quiet city, away from his slumbering people. The Athosians were relocated today, taking the urn that held Teyla's ashes, for she had not been buried on the land that would soon be abandoned. Bereavement had come, heavy and undesired, as John realised all he had left of her were a pair of sticks and memories.

Not enough, never enough. On his desk laid objects: sticks, a Satedan weapon, knives, a red t-shirt, a stack of Superman comics and a baseball cap. Teyla, Ronon, Elizabeth, Lorne, Ford. All he had were memories and stuff. A pile of stuff.

Crystal in hand, John made his way to the Chair room. He had yet to decide what it was he hoped to accomplish. Obsessed with the thought of threat neutralisation, he had followed Rodney everywhere, trying to get the crystal from him.

In the control room, in the communal room, in the infirmary, in the mess hall, in the corridors, Rodney walked, handling the crystal. Sometimes he took it out, stroking it with his thumb. Sometimes it stayed in his pocket, where he still stroked it, his hand moving against the fabric.

He didn't speak to anyone except to John, telling him all about the AI, about what they could do if only he would stop being so stubborn. There would be so much to accomplish, it seemed. Such conversations usually led to full-blown arguments that always ended with John reminding Rodney that he had murdered everyone. John was not proud of the fact he had gotten increasingly hurtful, but Rodney needed to realise what had happened! He just didn't seem to understand that science, knowledge and discovery did not matter anymore. They would be leaving the city as soon as the Daedalus arrived.

Of course, John still loved Atlantis, and wished to protect her, but the price they had paid was already too high. It would be a tremendous loss, but he was devoid of the capacity to feel it. Loss on top of loss on top of loss would only go so far. You couldn't feel what was beyond your capabilities, and John's emotions were as taxed as they were going to be. Still, destroying the city was a terrible thought and sometimes John caught himself thinking that perhaps there was another way.

Rodney insisted they could build ZPMs if only John sat in the Chair and looked for the way, the instructions. He was convinced he had to save the city. He mumbled about his plans, his job, his duty as Chief Science Officer and it enraged John to such a degree that he had had to consciously restrain himself from physically harming this man who had been one of his closest friend.

It would be too dangerous to sit in the Chair. Rodney didn't have a natural gene and if he wasn't in the Chair maybe the AI would think him a threat. John, in the deepest recesses of his mind, sometimes thought that to be confronted with the offer of threat neutralisation would be too much. He was afraid his anger would take over, afraid that the city, so intuitive, would know he thought Rodney a threat. Not that he was, not really, John knew it had been an accident, not a conscious decision on Rodney's part to activate the system that killed everyone. Nevertheless, perhaps the AI would pick up on his unease, his dirty, shameful thoughts, and would take matters into its own circuits.

John stopped walking. He stood still, in the middle of the corridor, looking down at the crystal in his hand. "What are you doing?" he asked himself. "What are you going to do?"

John resumed his walk to the Chair room. His pace had slowed, his hand held the crystal tighter. The door was in sight. Then he was stepping over the threshold, walking to the Chair.

Sitting in the Chair, the crystal still in his hand, he looked at its smooth sides. John knew where to put it, what to do.

ZPMs, fleet of ships, shields, defences were in this little piece of material.

Risk evaluation. Rodney, Atlantis, AI. All had the gene. Maybe if he sent Rodney with a marine to the mainland. A day, at the most, just to try.

What if he could preserve Atlantis? What if he could keep them all safe?

_I saw threat neutralisation and went with it_.

John twitched as Rodney's voice echoed in his head. He was not that guy, an at-all-costs kind of man. Rodney hadn't meant to kill them, it had been an accident, but if John knowingly sat in the Chair, tonight, it would not be.

Doranda had been an accident too. Just an accident, too many accidents. He trusted Rodney, didn't he? Rodney deserved that trust.

Rodney had deserved that trust. Accident. When they went back to Earth, what would be there for Rodney? Nothing, because John would not lie for him, would not hide the truth of the events, would have to say who had done what and when.

Rodney was a goner, no matter what. He was already gone, mumbling, shuffling, eyes shifty and dull. He only seemed like the old Rodney when he spoke to John, about the city and his plans.

John ran a hand through his hair. He breathed in deeply and stood from the Chair, staring at the crystal.

Threat neutralisation. Rodney, Atlantis, AI.

What would Rodney have, on Earth? Hadn't he said this was his home now, where he was meant to be, and he fully expected to die here? He would, too, were he left here. Left behind in a galaxy overrun by life-sucking monsters. Left to be caught? To talk? Give Earth away? Left to be a continued threat? No, John would not leave without Rodney. He never had and he never would.

Hadn't Rodney confided in John, told him he would be lost were he to go back to Earth, to go back to ho-hum life in what had become a foreign galaxy?

John looked at the Chair, then the crystal. Time for a decision had come along with the Daedalus. He had to talk with Rodney.

Slipping the crystal in his pocket, he hurried back to the communal room. Waking Rodney, John signalled for him to be quiet and follow him out of the room.

They walked to the mess hall in silence. John procured them each a cup of coffee before sitting across the way from Rodney.

He looked at the man, detailing the dirty, messy hair, the unkempt clothes, the red-rimmed eyes. "The Daedalus will be here soon."

"Yeah."

"You know I'll have to tell the SGC what happened."

"You don't have to. Carson won't say anything."

John stared down into the black depth of his cup and did not point out that Carson would tell the SGC the truth. They had discussed their options following Rodney's revelation in the Chair room, and had agreed that it was best to keep this to themselves. The other member of the expedition did not need to know what Rodney had done. Despite it all, John and Carson still felt Rodney deserved a measure of the courtesy long-term friendship allowed. "This isn't something I can disregard, Rodney. I'm sorry. I can't let you keep working, knowing what happened."

"Why? It was an accident. You know it was an accident!"

"It's the second accident. I wouldn't be…it wouldn't be right for me to let a third one happen."

The silence was heavy between the two men, until Rodney stood, the chair scrapping against the floor. "You're going to ruin my life."

John did Rodney the favour of looking up at him. He would not be a coward, not when he was destroying a friend. "I know."

They looked at each other in silence. Finally, Rodney spoke. "I could go through the gate. Let me go. I can…the outpost, or, we have allies–"

"You could get captured. You could talk and put the entire planet in danger." Shame ran through John's body. He had believed in Rodney, trusted him. He had thought him strong, brave, honourable, and sorely wished he still did.

"I wouldn't," Rodney said, softly, knowing it for the lie it was. "You can't make me do this. You can't! I didn't do anything! It was an accident!"

"I know."

"You're not the man I thought you were."

"Don't make this about me, Rodney."

"How can I not! Mister Pilot! Mister Natural Gene! Even Lyhal wanted you. I felt the pulse, you know! It came for me too! She spared me, but I'm just a substitute. She's waiting for you! She wants you, she wants to show you everything, and what do you do? You take the crystal and hide it away! You haven't been in the Chair. I know."

"No one is going in the Chair."

"You're taking everything from me."

"You're alive, aren't you? You have your life!"

Rodney's sharp intake of breath told John his point had been made, but Rodney's following words crushed that belief. "You don't have the right. This is a civilian mission; I'm high-ranking civilian officer. I'm leader here, not you! You can't do this! You don't have the power to do this, I do!"

John finished his coffee in one gulp and turned away from the table, from Rodney. He had tried, hoped Rodney would understand, but he hadn't. John suspected Rodney could not see the right way anymore. He saw only the AI and what it could offer. "There's no mission anymore. It's over. Go back to bed."

"Don't you walk away –"

"I said go back to bed." John had reached a decision and shared it with the principal concerned. He would not renege on his resolve, no matter how it might pain him to stay strong when faced with the enormity of the situation. For Rodney, consequences would be disastrous, but he was still alive. The only one to have survived. He was the cause of these woes, and as John remembered that, his breath caught and he wished he had never set foot on the ice of Antarctica.


	7. Chapter 7

**Chapter 7: Carry that weight**

"I'd like to thank you all for being here. I know that, wherever he is, Rodney would be pleased to see this. He'd hide it, but he'd be pleased that we're here, for him. Maybe a bit disbelieving that, even all these years after his disappearance, there are still people around who can't help but remember him." Jeanie takes a sip of wine, visibly overwhelmed by her emotion.

"I'm pleased for him that year after year, you come back. It seems like such a short time has passed when I look at you all, but it's too long a time to be without him…" Jeanie breaks off there, her lower lips trembling, her eyes moist. She smiles and a few of her guests laugh. "Next year I won't cry."

"Luv, that's what you've said every year, and I keep telling you next year he might be here and there won't be a need for tears." Carson lifts his glass and takes over the toast. "To us, who are here, who have survived and come home to tell the tales of those we knew."

John watches all the smiling faces, hears Carson's toast echoed in many voices. He looks at Jeanie who smiles, looks at Carson, busy telling a tale of the infirmary, carefully avoiding any mentions of strange, alien things, for Madison is without security clearance.

John looks at the faces: Miko, Williams, Miller, Latour, Carson, Carter, Jeanie, Kaleb, Madison. He notes Levin's absence, and thinks he should not have come either. He does not belong here, with Rodney's family, remembering him, trading stories. He downs his glass and pours himself another. No one will comment if John Sheppard gets wasted in honour of Rodney McKay, wherever he might be.

This is where John truly breaks. Not in Atlantis, knowing he is surrounded by death; not in Teyla's room, shutting her eyes; not in the control room, realising there are eight of them left; not on the Mainland, burying them all; not sitting on Ronon's bed, toying with his weapon, remembering how he longed for one, and barely able to stand the fact that he owns it.

Here. In Jeanie's home, surrounded by people he once knew, but still alone. Lost. It's quiet and private. He has had so many years of practice at hiding in plain sight that John knows no one has noticed this shift. No one can know that the last block fell into place. Just like that damnable cube they found so many years ago, John is hidden beyond layers of complicated coding. He is safe beneath his defences, for he will not allow anyone to try to break the code.

Inside, John is dying, desperate to run, hide, breakdown just once and allow his life to melt away. He wants the city back, he wants his people back, he wants his _family_ back and he aches. His heart and his soul, if he still possesses one, are deep, poisoned hole of pain.

Nevertheless, all the world knows is that John fills his glass and joins in Carson's mirthful enjoyment of Rodney on morphine.

**O-O-O-O-O**

The Daedalus was on its way. One day out, at the most.

The city was quiet, and once again, John watched Rodney get out of bed, taking care not to disturb anyone. He waited a few seconds before rising from his chair and following.

Rodney shuffled down the corridor, his socked feet muffling the sound of his steps. John watched him go, part worried, part disgusted.

What had happened to Rodney? How had he become this man without any of them noticing? Power, needs, wants, that was all that drove Rodney now. He did not realise why they had to go, said that the price had already been paid, they should be taking advantage of the opportunity they had.

John followed him to the living quarters. He hid when Rodney came back out of his room with mission gear. His clothes, his vest, his weapon. He had two backpacks and two hard-plastic cases. John gave him a few seconds advance and continued to trail him. Rodney had never gotten the knack of being aware of his surrounding in the city. He had felt safe, most of the time, claiming that the city was overflowing with marines who were there to protect his precious brain.

They made it to the control room without Rodney noticing John's presence. John stayed hidden by the corner and watched Rodney slowly make his way to the DHD.

He watched the gate dial, the address unfamiliar, but John had never been one to remember all the planets they visited.

He watched Rodney walk down the stairs. John drew close to the DHD as Rodney approached the gate. His heart was beating fast; his mind was a whirlwind of choices, possibilities. He watched Rodney walk away from him, from them and his mind screamed for him to act.

_Let him go! He won't be your problem anymore! He's a big boy and he can take care of himself. He obviously knows where he's going. He can get to an outpost and be safe. Maybe he will save the galaxy. There's nothing for him on Earth, he would be miserable._

_Raise the shield! Call out to him! He can't leave. He'll run into the Wraith, run into an enemy and betray Earth. It's dangerous out there, and you never leave a man behind. How will you live with yourself if you leave Rodney in Pegasus?_

Ironically, it was Rodney's voice that settled the matter. _I saw threat neutralisation and went with it._

John was used to listening to Rodney, taking his advice into consideration, trusting him.

As Rodney's back disappeared into the event horizon, John shut the gate.

Rodney's backpack fell to the floor, the straps severed.

John stood frozen, in the darkness of the control room. He breathed deeply in the stillness of the night, alone and lost.

**Fin**

I'm almost sorry for this. Almost :) Thank you very much for reading!


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